URLhttps://www.bco-dmo.org/dataset/626741
Download URLhttps://www.bco-dmo.org/dataset/626741/data/download
Media Type text/tab-separated-values
Created November 20, 2015
Modified August 19, 2016
State Final no updates expected
Brief Description

Elemental composition for 16S rRNA gene amplicon and metagenomic sequences

Acquisition Description

Analyses performed on “Mobio” IODP samples previously frozen at -80C. Reactive Fe and Mn were extracted using the citrate-dithionite method and measured on an ICP OES (Agilent Technologies 700 series axial). Analysis for TC, TN, and TS were determined using PE 2400 CN(S) analyzer. Analysis for TIC was determined by CM5014 CO2 coulometer with a CM5130 Acidification module. 

Processing Description

BCO-DMO Processing:
– Added cruise_id, lat and lon columns

Instruments

Instance Description

ICP OES (Agilent Technologies 700 series axial)

A spectrometer is an optical instrument used to measure properties of light over a specific portion of the electromagnetic spectrum.

Instance Description

PE 2400 CN(S) analyzer

Instruments that quantify carbon, nitrogen and sometimes other elements by combusting the sample at very high temperature and assaying the resulting gaseous oxides. Usually used for samples including organic material.

Instance Description

CM5014 CO2 coulometer with a CM5130 Acidification module.

A CO2 coulometer semi-automatically controls the sample handling and extraction of CO2 from seawater samples. Samples are acidified and the CO2 gas is bubbled into a titration cell where CO2 is converted to hydroxyethylcarbonic acid which is then automatically titrated with a coulometrically-generated base to a colorimetric endpoint.

Parameters

cruise_id [cruise_id]
Details
cruise_id
cruise identification
cruise designation; name
site [site]
Details
site
site identification
Sampling site identification.
lat [latitude]
Details
lat
latitude; north is positive

latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes

lon [longitude]
Details
lon
longitude; east is positive

longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datsets as degrees, minutes

core [sample]
Details
core
core identification

unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent

type [sample_type]
Details
type
type of sample: H = hole?
text description of type of sample collected (rock, bio, fluid, etc)
section [sample]
Details
section
core section identification

unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent

depth [depth]
Details
depth
depth below seafloor

Observation/sample depth below the sea surface. Units often reported as: meters, feet.


When used in a JGOFS/GLOBEC dataset the depth is a best estimate; usually but not always calculated from pressure; calculated either from CTD pressure using Fofonoff and Millard (1982; UNESCO Tech Paper #44) algorithm adjusted for 1980 equation of state for seawater (EOS80) or simply equivalent to nominal depth as recorded during sampling if CTD pressure was unavailable.

comments [comment]
Details
comments
molecular biology samples frozen at -80C
free text comments, may only have meaning to submitting PI
TC_pcent [unknown]
Details
TC_pcent
total carbon
association with a community-wide standard parameter is not yet defined
TN_pcent [unknown]
Details
TN_pcent
total nitrogen
association with a community-wide standard parameter is not yet defined
TS_pcent [unknown]
Details
TS_pcent
total sulfur
association with a community-wide standard parameter is not yet defined
TIC_pcent [unknown]
Details
TIC_pcent
total inorganic carbon
association with a community-wide standard parameter is not yet defined
TOC_pcent [TOC]
Details
TOC_pcent
total organic carbon
total organic Carbon
C_N [C_to_N]
Details
C_N
carbon:nitrogen ratio
Carbon to Nitrogen ratio; CAUTION; file dependent
CaCO3_pcent [CaCO3]
Details
CaCO3_pcent
calcium carbonate

Calcium Carbonate, in sediments as percent; or CaCO3 from water samples reported in various units; CAUTION measured in sediment and water column samples

Fe_pcent [Fe]
Details
Fe_pcent
percent reactive iron
Fe (Iron) concentration. May be reported in parts per million, nanomoles/Liter, or other units. Refer to dataset metadata for units.
Details
Fe_err

reactive iron standard deviation of duplicate extractions and analyses

Generic standard deviation value, taking on the units of the parameter that it is tied to.
Fe_RSD_pcent [standard deviation]
Details
Fe_RSD_pcent
iron % relative standard deviation: ratio of standard deviation to mean multiplied by 100 to express as percentage
Generic standard deviation value, taking on the units of the parameter that it is tied to.
Mn_pcent [Mn]
Details
Mn_pcent
percent reactive manganese

Mn (Manganese) concentration. May be reported in parts per million, nanomoles/Liter, or other units. Refer to dataset metadata for units.

Details
Mn_err

standard deviation of duplicate extractions and analyses for reactive manganese

Generic standard deviation value, taking on the units of the parameter that it is tied to.
Mn_RSD_pcent [standard deviation]
Details
Mn_RSD_pcent
manganese % relative standard deviation: ratio of standard deviation to mean multiplied by 100 to express as percentage
Generic standard deviation value, taking on the units of the parameter that it is tied to.

Dataset Maintainers

NameAffiliationContact
Jennifer B. GlassGeorgia Institute of Technology (Georgia Tech)
James McManusUniversity of Akron (UAkron)
Nancy CopleyWoods Hole Oceanographic Institution (WHOI BCO-DMO)

BCO-DMO Project Info

Project Title Functional gene diversity and expression in methane-hydrate bearing deep subsurface sediments
Acronym Methane-Hydrate Sediment Omics
URLhttps://www.bco-dmo.org/project/626690
Created November 19, 2015
Modified November 19, 2015
Project Description

Methane is a critical component of the deep subsurface. In shallow marine sediments, anaerobic oxidation of methane (AOM) is coupled to sulfate reduction. However, relatively little is known about which microbial metabolisms are active in deeply buried sediment containing methane hydrates, particularly with regard to alternative electron acceptors that could fuel deep AOM. We propose to determine which microbial population(s) and functional genes are active in the deep biosphere beneath Hydrate Ridge offshore Oregon by sequencing metagenomes and metatranscriptomes from samples drilled on ODP Leg 204 and archived for future molecular analysis. We will analyze gene diversity and expression in six geochemically distinct zones from 2 to 139 meters below the seafloor with the goal of evaluating the relationship between geochemical conditions (i.e. sulfate, iron and manganese availability) and microbial metabolic activity.

Related References:

Tréhu, A.M, Bohrmann, G., Rack, F.R., Torres, M.E., et al., 2003. Proc. ODP, Init. Repts., 204: College Station, TX (Ocean Drilling Program).doi:10.2973/odp.proc.ir.204.2003

Shipboard Scientific Party, 2003. Site 1244. In Tréhu, A.M, Bohrmann, G., Rack, F.R., Torres, M.E., et al., Proc. ODP, Init. Repts., 204: College Station, TX (Ocean Drilling Program), 1–132. doi:10.2973/odp.proc.ir.204.103.2003

Tréhu, A.M., Bohrmann, G., Torres, M.E., and Colwell, F.S. (Eds.), 2006. Proc. ODP, Sci. Results, 204: College Station, TX (Ocean Drilling Program). doi:10.2973/odp.proc.sr.204.2006

This work was supported by a C-DEBI Research Grant.

Data Project Maintainers
NameAffiliationRole
Jennifer B. GlassGeorgia Institute of Technology (Georgia Tech)Principal Investigator
Cecilia Batmalle KretzGeorgia Institute of Technology (Georgia Tech)Co-Principal Investigator
James McManusUniversity of Akron (UAkron)Scientist
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